- The objectives of this study were to: 1) determine how organic matter (incorporated vs. surface mulch) and nitrogen fertilization rate impact northern highbush blueberry (Vaccinium corymbosum L.) plant biomass, carbon accumulation, plant losses and allocation, and mycorrhizal infection in mature plants, and 2) determine the magnitude of carbon fluxes (carbon net primary production (NPP), soil respiration, and fruit and pruning exports) and stocks within a blueberry production system, and how these are affected by typical management practices. Treatments were in effect for nine years since planting establishment; here we report on data collected in 2011 and 2012. Many of these treatments seem to have short- and long-term effects on blueberry plants. Long-term effects included the impact of pre-planting incorporation of sawdust, which as a main effect, had an overall positive effect on yield, and soil fertility, with all soil nutrients being above recommended sufficiency levels for blueberry production. Soil pH was increased by incorporation, and was affected by an incorporation by mulch interaction where incorporated bare plots had the highest pH, and the largest average plant dry weight and carbon (C) mass (3.5 and 1.7 kg/plant, respectively) despite the pH being above the recommended level for blueberry production. Incorporated plots in general, had a higher total field C stock averaging 97.6 t·ha ⁻¹ for mulched plots and 93.7 t·ha⁻¹ for bare plots. Mulching as a C stock contributed 12.3 t·ha⁻¹, 13% of the total C stock. Mulching as main treatment effect was not found to be beneficial in terms of increasing plant and soil C stocks. Although mulching did increase soil organic C in 2012, this did not seem to affect total soil C stocks, perhaps because soil respiration was also increased by the mulch. Nitrogen fertilizer rate did not affect plant biomass or C stock, nor did it affect soil C stocks and nutrients. Net primary productivity averaged 588 g·m⁻².year and was not affected by the treatments, although incorporated plots had about 25% more NPP than non-incorporated plots. Our results have illustrated that with a goal of optimizing plant growth, yield, and C stocks, blueberry production systems that include pre-plant incorporation of organic matter without addition of surface mulch and moderate rates of nitrogen fertilizer are best. In addition, a between-row perennial grass cover crop is recommended to increase field C stocks and to limit soil erosion. The information gathered in this study can be used to estimate the contribution of C storage in temperate perennial crops to global C stocks. Recommended management practices could lead to a policy system where farmers receive incentives for sustainable low C agriculture.